Dear All,
İ want to prepare a library of compounds for virtual screening. But I keep running into multiple issues that are already resolved but when I apply the solutions on my compounds, nothing seems to work.
1. There are no z-coordinates in the SDF files I downloaded from the Enamine database. How do I add them.
2. The obabel command line does not open these files from enamine. Gives varıous errors that I checked online. Some are related to the shell and some to the bugs in the software.
3. İs there any other software or method to generate these compound structures.
4. Any idea how to download a specific library from ZINC database. such as only the FDA approved compounds?
I shall be grateful for the help.
Thank you
Best regards
Ayesha Fatima
I will try to address one by one
For 1 and 2 quiery.
Ttry with other Tools, i,e
Jmol: Jmol is a free and open-source molecular visualization tool that can be used to open SDF files and add z-coordinates.
Another simple tool is DataWarrior can be used to convert csv file or smiles
2. To download a specific library from the ZINC database, you have to ZINC Tranche Browser. Then filter the ZINC database by a variety of criteria, including drug-likeness, lead-likeness, and FDA approval status. You can use below link to get FDA drug directly from ZINC
https://zinc15.docking.org/substances/subsets/fda/